Table 3.
Short table of genomic statistics for Pseudomonas corrugata and P. mediterranea strains under study.
| P. corrugata | P. mediterranea | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| CFBP5403 | CFBP5454 | NCPPB2445 | TEIC1148 | CFBP5404 | CFBP5444 | CFBP5447 | TEIC1022 | TEIC1105 | |
| Total number of reads | 11,800,202 | 8,420,692 | 1,519,930 | 8,608,470 | 1,209,534 | 1,394,308 | 24,635,686 | 1,276,402 | 23,866,648 |
| Average read length | 35 | 70.6 | 145 | 35 | 145 | 145 | 51 | 145 | 44 |
| Total bases | 413,007,070 | 594,525,036 | 220,389,850 | 301,296,450 | 175,382,430 | 202,174,660 | 1,256,357,465 | 185,078,290 | 1,040,233,200 |
| DNA, total number of bases in contigs | 6,166,582 | 6,195,615 | 6,084,011 | 6,266,776 | 6,281,542 | 6,298,862 | 6,270,666 | 6,231,327 | 6,299,426 |
| Ambiguous bases | 39,282 | 2299 | 3749 | 31,312 | 3143 | 3499 | 18 | 11,988 | 1,651 |
| Percentage of ambiguous bases | 0.64 | 0.04 | 0.06 | 0.50 | 0.05 | 0.06 | 0.00 | 0.19 | 0.03 |
| DNA coding number of bases | 5,471,555 | 5,491,990 | 5,391,923 | 5,567,198 | 5,564,235 | 5,572,667 | 5,573,461 | 5,507,149 | 5,573,467 |
| DNA G+C number of bases | 3,706,298 | 3,747,457 | 3,686,460 | 3,763,425 | 3,846,554 | 3,853,935 | 3,862,577 | 3,813,571 | 385,5401 |
| GC content (%) | 60.1 | 60.5 | 60.6 | 60.1 | 61.2 | 61.2 | 60.7 | 61.2 | 61.2 |
| Total number of contigs | 442 | 84 | 104 | 432 | 150 | 89 | 47 | 101 | 91 |
| N75 | 17,365 | 48,599 | 85,837 | 16,551 | 11,1354 | 118,717 | 447,675 | 83,242 | 120,020 |
| N50 | 29,882 | 79,475 | 202,143 | 32,179 | 188,131 | 229,164 | 662,701 | 142,363 | 230,696 |
| Genes total number | 5912 | 5570 | 5463 | 5845 | 5652 | 5638 | 5533 | 5594 | 5643 |
| Coding density (%) | 87.9 | 88.5 | 88.4 | 88.4 | 88.4 | 88.3 | 88.4 | 88.1 | 88.3 |
| Completeness (%) | 97.02 | 99.69 | 99.68 | 99.14 | 99.69 | 99.68 | 99.69 | 99.45 | 99.69 |
| Contamination (%) | 0.80 | 0.42 | 0.45 | 0.47 | 0.48 | 0.79 | 0.48 | 0.43 | 0.79 |
| Protein coding genes | 5809 | 5443 | 5313 | 5737 | 5515 | 5484 | 5786 | 5450 | 5481 |
| RNA genes | 103 | 127 | 150 | 108 | 137 | 154 | 135 | 144 | 162 |
| Protein coding genes with function prediction | 4812 | 4621 | 4516 | 4753 | 4608 | 4598 | 4804 | 4611 | 4606 |
| Protein coding genes without function prediction | 997 | 822 | 797 | 984 | 907 | 886 | 982 | 839 | 875 |
| Protein coding genes for enzymes | 1307 | 1355 | 1341 | 1331 | 1339 | 1339 | 1312 | 1337 | 1339 |
| w/o enzymes but with candidate KO based enzymes | 147 | 19 | 26 | 68 | 17 | 11 | 130 | 24 | 13 |
| Protein coding genes connected to transporter classification | 832 | 792 | 777 | 810 | 790 | 791 | 809 | 785 | 791 |
| Protein coding genes connected to KEGG pathways | 1497 | 1564 | 1546 | 1536 | 1565 | 1570 | 1523 | 1538 | 1570 |
| Protein coding genes connected to KEGG Orthology (KO) | 2733 | 2850 | 2807 | 2808 | 2833 | 2828 | 2760 | 2804 | 2828 |
| Protein coding genes connected to MetaCyc pathways | 1272 | 1325 | 1311 | 1300 | 1313 | 1313 | 1287 | 1312 | 1313 |
| Protein coding genes with COGs | 3839 | 4012 | 3927 | 3923 | 3965 | 3979 | 3927 | 3949 | 3978 |
| Chromosomal cassettes | 717 | 532 | 508 | 697 | 556 | 562 | 613 | 560 | 559 |
| Biosynthetic clusters | 39 | 46 | 38 | 45 | 49 | 50 | 44 | 46 | 43 |
| Genes in biosynthetic clusters | 289 | 386 | 332 | 331 | 397 | 410 | 389 | 405 | 369 |
| COG clusters | 2033 | 2051 | 2046 | 2053 | 2037 | 2039 | 2026 | 2026 | 2039 |
| KOG clusters | 841 | 841 | 852 | 852 | 837 | 839 | 840 | 845 | 839 |
| Pfam clusters | 2601 | 2566 | 2551 | 2597 | 2,547 | 2,551 | 2,577 | 2,547 | 2,550 |
| TIGRfam clusters | 1345 | 1362 | 1355 | 1369 | 1369 | 1372 | 1365 | 1362 | 1372 |
For the full table refer to the supporting material (Supplementary File 1). TEIC, Technological Educational Institute of Crete Bacterial collection; CFBP, International Center for Microbial Resources, French Collection for Plant-associated Bacteria, INRA, Angers, France; NCPPB, National Collection of Plant Pathogenic Bacteria, Fera, York, U.K. Isolate names followed by the letter “T” are type strains.